StepWiseRNA_FloatingBase_Sampler_Util.cc File Reference

#include <protocols/swa/rna/StepWiseRNA_Util.hh>
#include <protocols/swa/rna/StepWiseRNA_FloatingBase_Sampler_Util.hh>
#include <protocols/swa/rna/StepWiseRNA_RotamerGenerator_Wrapper.hh>
#include <protocols/swa/rna/StepWiseRNA_RotamerGenerator_Wrapper.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_Base_Sugar_Rotamer.hh>
#include <protocols/swa/rna/StepWiseRNA_Base_Sugar_Rotamer.fwd.hh>
#include <core/scoring/rna/RNA_FittedTorsionInfo.hh>
#include <core/scoring/rna/RNA_Util.hh>
#include <protocols/rna/RNA_LoopCloser.hh>
#include <protocols/swa/rna/StepWiseRNA_JobParameters.hh>
#include <protocols/swa/rna/StepWiseRNA_VDW_Bin_Screener.hh>
#include <protocols/swa/rna/StepWiseRNA_VDW_Bin_Screener.fwd.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/id/TorsionID.hh>
#include <basic/Tracer.hh>
#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/AtomType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/pose/Pose.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/io/silent/SilentFileData.fwd.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/BinaryRNASilentStruct.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rna/RNA_TorsionPotential.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/util.hh>
#include <set>
#include <numeric/conversions.hh>
#include <numeric/NumericTraits.hh>
#include <iostream>
#include <fstream>
#include <sstream>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/EnergyMap.fwd.hh>

Go to the source code of this file.

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::swa
	protocols::swa::rna

Constant Groups
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::swa
	protocols::swa::rna

Functions
static basic::Tracer	TR ("protocols.swa.rna.stepwise_rna_floating_base_sampler_util")
bool	protocols::swa::rna::Is_base_stack (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list, core::Real const base_axis_CUTOFF, core::Real const base_planarity_CUTOFF)
bool	protocols::swa::rna::Is_base_pair (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list, core::Real const base_axis_CUTOFF, core::Real const base_planarity_CUTOFF)
bool	protocols::swa::rna::Is_strong_base_stack (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list)
bool	protocols::swa::rna::Is_medium_base_stack_and_medium_base_pair (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list)
bool	protocols::swa::rna::Base_centroid_screening (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list, Size const num_nucleotides, SillyCountStruct &count_data, bool const allow_base_pair_only_screen)
core::kinematics::Stub	protocols::swa::rna::Get_ribose_stub (conformation::Residue const &rsd, bool const Is_prepend, bool const verbose)
Base_bin	protocols::swa::rna::Get_euler_stub_bin (numeric::xyzVector< core::Real > const &centriod, Euler_angles const &euler_angles)
int	protocols::swa::rna::DOF_bin_value (std::map< Base_bin, int, compare_base_bin >::const_iterator const &base_bin_it, std::string const &DOF)
Real	protocols::swa::rna::DOF_bin_size (std::string const &DOF)
void	protocols::swa::rna::Analyze_base_bin_map (std::map< Base_bin, int, compare_base_bin > const &base_bin_map, std::string const &DOF_one, std::string const &DOF_two, std::string const foldername)
void	protocols::swa::rna::Analyze_base_bin_map (std::map< Base_bin, int, compare_base_bin > const &base_bin_map, std::string const foldername)
Euler_angles	protocols::swa::rna::Get_euler_angles (numeric::xyzMatrix< core::Real > const &coordinate_matrix)
void	protocols::swa::rna::convert_euler_to_coordinate_matrix (Euler_angles const &E, numeric::xyzMatrix< core::Real > &coordinate_matrix)
void	protocols::swa::rna::translate_then_rotate_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &vector, numeric::xyzMatrix< core::Real > const matrix, bool const verbose)
void	protocols::swa::rna::set_to_origin (pose::Pose &pose, Size const seq_num, bool verbose)
void	protocols::swa::rna::get_specific_atom_coordinate (std::string const &atom_name, numeric::xyzVector< core::Real > &atom_pos, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)
core::Real	protocols::swa::rna::get_max_centroid_to_atom_distance (utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, std::string const atom_name)
utility::vector1 < core::conformation::ResidueOP >	protocols::swa::rna::setup_residue_at_origin_list (pose::Pose const &pose, Size const &moving_res, bool const extra_anti_chi_rotamer, bool const extra_syn_chi_rotamer, std::string const pose_name)
bool	protocols::swa::rna::check_floating_base_chain_closable (core::Size const &reference_res, utility::vector1< pose_data_struct2 > pose_data_list, utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, core::kinematics::Stub const &moving_res_base_stub, bool const Is_prepend, core::Size const gap_size)
bool	protocols::swa::rna::check_floating_base_chain_closable (core::Size const &reference_res, core::pose::Pose const &pose, utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, core::kinematics::Stub const &moving_res_base_stub, bool const Is_prepend, Size const gap_size)
void	protocols::swa::rna::set_base_coordinate_frame (pose::Pose &pose, Size const &seq_num, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)

Function Documentation

static basic::Tracer TR ( "protocols.swa.rna.stepwise_rna_floating_base_sampler_util"  )

static